Genome-wide analysis of long non-coding RNAs under diel light exhibits role in floral development and the circadian clock in Arabidopsis thaliana

Oct 18, 2022International journal of biological macromolecules

Long non-coding RNAs linked to flower growth and daily biological clock under light cycles in Arabidopsis

AI simplified

Circadian Biology on OpenScience ↗PubMed ↗DOI ↗

Abstract

A total of 968, 1050, and 998 long non-coding RNAs (lncRNAs) were identified at 8 h light, 16 h light, and 8 h dark conditions, respectively.

Unique lncRNAs were observed at different light conditions, with 423 at 8 h light, 486 at 16 h light, and 417 at 8 h dark.
Common lncRNAs across all conditions totaled 334.
Identified lncRNAs exhibited lower expression levels and were less GC-rich compared to protein-coding mRNAs.
Enriched motifs in lncRNA transcribing regions were linked to light-responsive genes, flower development, and circadian rhythms.
Certain lncRNAs were predicted to interact with miRNAs that influence developmental processes and transcription regulation.
lncRNA transcribing regions showed enrichment for specific epigenetic marks and depletion for heterochromatic and repressive histone modifications.

AI simplified

The circadian clock is regulated by signaling networks that enhance a plant's ability to coordinate internal events with the external environment. In this study, we examine the rhythmic expression of long non-coding RNAs (lncRNAs) using multiple transcriptomes of Arabidopsis thaliana in the diel light cycle and integrated this information to have a better understanding of the functions of lncRNAs in regulating the circadian clock. We identified 968, 1050, and 998 lncRNAs at 8 h light, 16 h light and 8 h dark conditions, respectively. Among these, 423, 486, and 417 lncRNAs were uniquely present at 8 h light, 16 h light, and 8 h dark, respectively, whereas 334 lncRNAs were common under the three conditions. The specificity of identified lncRNAs under different light conditions was verified using qRT-PCR. The identified lncRNAs were less GC-rich and expressed at a significantly lower level than the mRNAs of protein-coding genes. In addition, we identified enriched motifs in lncRNA transcribing regions that were associated with light-responsive genes (SORLREP and SORLIP), flower development (AGAMOUS), and circadian clock (CCA1) under all three light conditions. We identified 10 and 12 different lncRNAs targeting different miRNAs with perfect and interrupted complementarity (endogenous target mimic). These predicted lncRNA-interacting miRNAs govern the function of a set of genes involved in the developmental process, reproductive structure development, gene silencing and transcription regulation. We demonstrated that the lncRNA transcribing regions were enriched for epigenetic marks such as H3.3, H3K4me2, H3K4me3, H4K16ac, H3K36ac, H3K56ac and depleted for heterochromatic (H3K9me2 and H3K27me1) and repressive (H3K27me3) histone modifications. Further, we found that hypermethylated genomic regions negatively correlated with lncRNA transcribing regions. Overall, our study showed that lncRNAs expressed corresponding to the diel light cycle are implicated in regulating the circadian rhythm and governing the developmental stage-specific growth.

Full Text

Full text is available at the source.

View full text (XML) ↗View full text ↗

Genome-wide analysis of long non-coding RNAs under diel light exhibits role in floral development and the circadian clock in Arabidopsis thaliana

Abstract

Full Text

You found one interesting study. We’ll send the next 7.

what lands in your inbox each week:

Recent issues from the circadian biology brief

Abstract

Full Text

Related papers

You found one interesting study. We’ll send the next 7.

what lands in your inbox each week:

Recent issues from the circadian biology brief